Abstract
Restriction-Modification systems (RMS) are one of the main mechanisms of defence against foreign DNA invasion and can have an important role in the regulation of gene expression. The obligate human pathogen Neisseria gonorrhoeae carries one of the highest loads of RMS in its genome; between 13 to 15 of the three main types. Previous work has described their organization in the reference genome FA1090 and has inferred the associated methylated motifs. Here, we studied the structure of RMS and target methylated motifs in 25 gonococcal strains sequenced with Single Molecule Real-Time (SMRT) technology, which provides data on DNA modification. The results showed a variable picture of active RMS in different strains, with phase variation switching the activity of Type III RMS, and both the activity and specificity of a Type I RMS. Interestingly, the Dam methylase was found in place of the NgoAXI endonuclease in two of the strains, despite being previously thought to be absent in the gonococcus. We also identified the real methylation target of NgoAXII as 5′-GCAGA-3′, different from that previously described. Results from this work give further insights into the diversity and dynamics of RMS and methylation patterns in N. gonorrhoeae.
Highlights
N. gonorrhoeae is among the bacterial species with the highest numbers of Restriction-Modification systems (RMS) despite being naturally competent for DNA uptake[7]
From 13 to 15 complete RMS were found in each of the 25 N. gonorrhoeae strains included in the study (Supplementary Table 1): 2 of Type I, 11 of Type II and 2 of Type III, all of which are present in the REBASE database (Fig. 1)
The amino acid translation of the repetitive region in the two Type III RMS is rich in prolines and, interestingly, the ppiA gene upstream of the methylase in NgoAX is an isomerase that catalyzes the isomerization of peptide bonds in prolyl residues, assisting protein folding[25]
Summary
N. gonorrhoeae is among the bacterial species with the highest numbers of RMS despite being naturally competent for DNA uptake[7]. RMS have been associated with other roles apart from defending the genome against foreign DNA invasion, such as being involved in the epigenetic control of gene expression[8,9,10] They have been described as selfish elements, tending to propagate on mobile genetic elements and promoting their own survival[13]. The Dam MTase participates in the methyl-directed DNA mismatch repair system and this constrains the flexibility of the bacteria to undergo phase variation, which involves mispairing of bases during replication slippage[23] It has been found in some N. lactamica and N. meningitidis strains[24], there have been no reports of N. gonorrhoeae carrying this enzyme until now. Results from this study give a more comprehensive insight into the link between genomics and epigenomics in the gonococcus
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